The most common definition: All the messenger RNA (mRNA) molecules transcribed from the genome. [More]

Varies with the differentiated state of the cell and the activity of the transcription factors that turn gene transcription on (and off).

Speaking strictly, one would define the transcriptome as all the RNA molecules — which includes a wide variety of untranslated, nonprotein-encoding RNA [Link to examples] — transcribed from the DNA of the genome. It is now thought that ~75% of our DNA is transcribed into RNA although only 1.5% of this is messenger RNA for protein synthesis.

addition of phosphate groups to some of the amino acids in the protein [Examples];

etc.

While we humans probably have only some 21 thousand genes, we probably can make at least 10 times that number of different proteins. The great majority of our genes produce pre-mRNAs that are alternatively-spliced.

The study of proteomics is important because proteins are responsible for both the structure and the functions of all living things. Genes are simply the instructions for making proteins. It is proteins that make life.

At any one time, a human cell might contain some 10,000 different proteins; some (e.g. ribosomal proteins) in great abundance, others (e.g. transcription factors) in lower numbers.

The set of proteins within a cell varies

from one differentiated cell type to another (e.g. red blood cell vs lymphocyte) and

the DNA encoding the DNA-binding domain of a transcription factor needed to turn on expression of a "reporter gene" such as the lacZ gene that encodes the enzyme β-galactosidase coupled to

the DNA encoding the "target" protein; that is, the protein whose possible partners you wish to identify.

Insert the plasmid into living haploid yeast of one mating type (e.g., a)

Using the same methods, create many different plasmids each containing

the DNA encoding the activation domain of the transcription factor;

the DNA encoding a possible partner ("bait") protein. (With the help of automated equipment, you can even make plasmids representing each of the entire ~6,000-gene genome of yeast.)

Insert each of these plasmids into α yeast cells and grow them as separate clones.

Mate each α clone with the target clone (a).

If the fusion protein produced by the transcription and translation of a "bait"-containing plasmid
can bind to the fusion protein containing the target,

the two domains of the transcription factor can interact to turn on expression of the reporter gene (lacZ in our case).

Grown on an indicator substrate, these colonies will turn blue. [Another example]

The DNA in these colonies can then be isolated and sequenced.

The result: identification of the proteins that can associate with the target protein.

Using the two-hybrid method, it has been possible to identify many sets of interacting proteins in yeast and other organisms. (The 23 September 2005 issue of Cell reports the identification of over 3000 interactions among pairs of human proteins.